Electron diffraction tomography (EDT) has gained increasing interest, starting with the development of automated electron diffraction tomography (ADT) which enables the collection of three-dimensional electron diffraction data from nano-sized crystals suitable for ab initio structure analysis. A basic description of the ADT method, nowadays recognized as a reliable and established method, as well as its special features and general applicability to different transmission electron microscopes is provided. In addition, the usability of ADT for crystal structure analysis of single nano-sized crystals with and without special crystallographic features, such as twinning, modulations and disorder is demonstrated.

Strain tensor measurements are important for understanding elastic and plastic deformation, but full bulk strain tensor measurement techniques are still lacking, in particular for dynamic loading. Here, such a methodology is reported, combining imaging-based strain field mapping and simultaneous X-ray diffraction for four typical loading modes: one-dimensional strain/stress compression/tension. Strain field mapping resolves two in-plane principal strains, and X-ray diffraction analysis yields volumetric strain, and thus the out-of-plane principal strain. This methodology is validated against direct molecular dynamics simulations on nanocrystalline tantalum. This methodology can be implemented with simultaneous X-ray diffraction and digital image correlation in synchrotron radiation or free-electron laser experiments.

This article describes a high-efficiency experimental configuration for a self-referenced lattice comparator with a `brush beam' of synchrotron radiation from a bending magnet and two linear position-sensitive photon-counting-type X-ray detectors. The efficiency is more than ten times greater compared with the `pencil-beam' configuration and a pair of zero-dimensional detectors. A solution for correcting the systematic deviation of d-spacing measurements caused by the horizontal non-uniformity of the brush beam is provided. Also, the use of photon-counting-type one-dimensional detectors not only improves the spatial resolution of the measurements remarkably but can also adjust the sample's attitude angles easily.

The room-temperature experiment has been revisited for macromolecular crystallography. Despite being limited by radiation damage, such experiments reveal structural differences depending on temperature, and it is expected that they will be able to probe structures that are physiologically alive. For such experiments, the humid-air and glue-coating (HAG) method for humidity-controlled experiments is proposed. The HAG method improves the stability of most crystals in capillary-free experiments and is applicable at both cryogenic and ambient temperatures. To expand the thermal versatility of the HAG method, a new humidifier and a protein-crystal-handling workbench have been developed. The devices provide temperatures down to 4°C and successfully maintain growth at that temperature of bovine cytochrome c oxidase crystals, which are highly sensitive to temperature variation. Hence, the humidifier and protein-crystal-handling workbench have proved useful for temperature-sensitive samples and will help reveal temperature-dependent variations in protein structures.

Rotation is a core crystallographic operation. Two sets of Cartesian coordinates of each point of a rotated object, those before and after rotation, are linearly related, and the coefficients of these linear combinations can be represented in matrix form. This 3 × 3 matrix is unique for all points and thus describes unambiguously a particular rotation. However, its nine elements are mutually dependent and are not interpretable in a straightforward way. To describe rotations by independent and comprehensible parameters, crystallographic software usually refers to Euler or to polar angles. In crystallography and cryo-electron microscopy, there exists a large choice of conventions, making direct comparison of rotation parameters difficult and sometimes confusing. The program py_convrot, written in Python, is a converter of parameters describing rotations. In particular, it deals with all possible choices of polar angles and with all kinds of Euler angles, including all choices of rotation axes and rotation directions. Using a menu, a user can build their own rotation parameterization; its action can be viewed with an interactive graphical tool, Demo. The tables in this article and the extended help pages of the program describe details of these parameterizations and the decomposition of rotation matrices into all types of parameters. The program allows orthogonalization conventions and symmetry operations to be taken into account. This makes the program and its supporting materials both an illustrative teaching material, especially for non-specialists in mathematics and computing, and a tool for practical use.

Microcrystal delivery methods are pivotal in the use of serial femtosecond crystallography (SFX) to resolve the macromolecular structures of proteins. Here, the development of a novel technique and instruments for efficiently delivering microcrystals for SFX are presented. The new method, which relies on a one-dimensional fixed-target system that includes a microcrystal container, consumes an extremely low amount of sample compared with conventional two-dimensional fixed-target techniques at ambient temperature. This novel system can deliver soluble microcrystals without highly viscous carrier media and, moreover, can be used as a microcrystal growth device for SFX. Diffraction data collection utilizing this advanced technique along with a real-time visual servo scan system has been successfully demonstrated for the structure determination of proteinase K microcrystals at 1.85 Å resolution.

A new temperature-controllable humidifier for X-ray diffraction has been developed. It is shown that the humidifier can successfully maintain protein crystal growth at a temperature lower than room temperature.

The Python-based program py_convrot is a universal converter of rigid-body rotation parameters. The program interactively illustrates the action of various rotation parameters and can be used both for teaching goals and for practical applications.

A new approach to variable-temperature measurements is presented, where the sample temperature changes continuously as a function of position.

This article presents the capability of the QMAX furnace, devoted to reciprocal space mapping through X-ray scattering at high temperature up to 2000 K.

A portable small-angle X-ray scattering instrument with geometrical dimensions suitable for installation at the D22 instrument was designed and constructed for simultaneous small-angle X-ray and neutron scattering experiments at ILL.

An algorithm, based on the matching of q-vectors pairs, is combined with three-dimensional pattern matching using a nearest-neighbors approach to index Laue and monochromatic serial crystallography data recorded on small unit cell samples.

Archaea are motile by the rotation of the archaellum. The archaellum switches between clockwise and counterclockwise rotation, and movement along a chemical gradient is possible by modulation of the switching frequency. This modulation involves the response regulator CheY and the archaellum adaptor protein CheF. In this study, two new crystal forms and protein structures of CheY are reported. In both crystal forms, CheY is arranged in a domain-swapped conformation. CheF, the protein bridging the chemotaxis signal transduction system and the motility apparatus, was recombinantly expressed, purified and subjected to X-ray data collection.

Describing his project of counting bears, bobcats and other predatory mammals along the Appalachian Trail, National Zoological Park wildlife ecologist William McShea looks to American literature for a comparison.

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Water is a critical molecule for human life, and, because it is abundant in space, it also plays an important role in the life of […]

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In addition to the species name, Leafsnap provides high-resolution photographs and information about the tree's flowers, fruit, seeds and bark—giving the user a comprehensive understanding of the specie

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A new study has revealed information about the way tungara frogs in the tropical rain forest hear, sort, and process sounds which is very similar to the way humans do. The knowledge could be applicable to communication disorders associated with hearing loss and attention deficits or difficulties.

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The Smithsonian Tropical Research Institute has released the first completely portable bilingual species identification guide for the shore fishes of the tropical Eastern Pacific as a free iPhone application.

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Recent geologic mapping of the Medusae Fossae Formation on Mars—an intensely eroded deposit near the northern edge of the cratered highlands—has revealed a wider distribution of its western component than was previously recognized.

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With the tap of a finger, keepers are introducing the Zoo’s six orangutans to iPads, which provide unique stimuli.

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Unique among Earth’s creatures, turtles are the only animals to form a shell on the outside of their bodies through a fusion of modified ribs, […]

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Hot spots of mercury pollution in aquatic sediments and soils can contaminate local food webs and threaten ecosystems, but cleaning them up can be expensive […]

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  The surface of Venus is hidden beneath a perpetual blanket of clouds, but radar allows scientists at the National Air and Space Museum to […]

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Native Americans and America’s early colonists ate many more blue crabs than modern researchers previously thought, according to a team of scientists studying crab remains […]

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Point your smartphone at the skeleton of a vampire bat mounted in a museum case, wait a minute and you will see it wiggle, jump […]

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Geologic mapping is an integral part of exploration and understanding a planetary landscape, because it shows the relationships between geologic units and helps delineate the […]

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Tiny Anolis lizards preserved since the Miocene in amber are giving scientists a true appreciation of the meaning of community stability. Dating back some 15 […]

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Salamanders are typically elusive animals and adept at hiding, but National Zoo visitors will have a chance to see a variety of different amphibian species […]

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Snowstorms and blizzards send people to raid supermarkets and prepare their homes for days of staying indoors, but how do the animals at the Smithsonian’s […]

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New fossils found in Northeastern China have revealed a remarkable evolutionary coincidence: an extinct group of insects known as Kalligrammatid lacewings (Order Neuroptera) share an […]

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With over 138 million collection objects, 2.1 million library volumes, and 137,000 cubic feet of archives, the stories of how our collections have made their […]

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In conflicts between predators and prey, speed is a decided advantage, and evolution has given the trap-jaw ant a distinct advantage with spring-loaded jaws that […]

The post Locked and loaded: unique trigger design fires this ant’s snapping jaws appeared first on Smithsonian Insider.

“Probably no genus of birds in the American avifauna has received the amount of attention that has been bestowed upon the turkeys…there has been no […]

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Flying through the air? Check. Surviving snake bites? Check. One of the most adorable creatures on earth? Absolutely! Do you think you know everything about […]

The post This Squirrel Appreciation Day we have a few surprising squirrely facts for you appeared first on Smithsonian Insider.

Every day, astronomers at the Harvard-Smithsonian Center for Astrophysics depend on computers to help them solve the mysteries of the universe, just as they did […]

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M. Pinar and M. A. Penalva

TRAnsport Protein Particle (TRAPP) complexes regulate membrane traffic. TRAPPII and TRAPPIII share a core hetero-heptamer, also denoted TRAPPI. In fungi TRAPPIII and TRAPPII mediate GDP exchange on RAB1 and RAB11, respectively, regulating traffic across the Golgi, with TRAPPIII also activating RAB1 in autophagosomes. Our finding that Aspergillus nidulans TRAPPII can be assembled by addition of a TRAPPII-specific subcomplex onto core TRAPP prompted us to investigate the possibility that TRAPPI/TRAPPIII already residing in the Golgi matures into TRAPPII to determine a RAB1-to-RAB11 conversion as Golgi cisternae progress from early Golgi to TGN identity. By time-resolved microscopy we determine that the TRAPPII reporter Trs120/TRAPPC9 is recruited to existing TGN cisternae slightly before RAB11 arrives, and resides for~45 sec on them before cisternae tear off into RAB11 secretory carriers. Notably, the core TRAPP reporter Bet3/TRAPPC3 was not detectable in early Golgi cisternae, being instead recruited to TGN cisternae simultaneously with Trs120/TRAPPC9, indicating en bloc recruitment of TRAPPII to the Golgi and arguing strongly against the TRAPP maturation model.

On Monday, Aug. 21, beginning shortly after 9 a.m. Pacific Time, the sky will darken across North America as the moon’s orbit carries it between […]

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A novel approach for finding and evaluating structural models of small metallic nanoparticles is presented. Rather than fitting a single model with many degrees of freedom, libraries of clusters from multiple structural motifs are built algorithmically and individually refined against experimental pair distribution functions. Each cluster fit is highly constrained. The approach, called cluster-mining, returns all candidate structure models that are consistent with the data as measured by a goodness of fit. It is highly automated, easy to use, and yields models that are more physically realistic and result in better agreement to the data than models based on cubic close-packed crystallographic cores, often reported in the literature for metallic nanoparticles.

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If a supernova vaporized Earth’s ozone layer, what would happen to life in the ocean? Smithsonian biologist Pat Neale shows how UV rays could harm […]

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myVolcano is a crowd-sourcing app that enables you to share your photographs and descriptions of volcanic hazards, as well as collecting samples and measurements of […]

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The Smithsonian’s National Museum of Natural History released a new mobile app “Skin and Bones” Jan. 13. The free app is available for download in […]

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Happy Holidays from the Smithsonian’s National Air and Space Museum!

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 The zoo extends the collecting mission of the Smithsonian into the realm of the living. From the Series: Stories From the Vault: Random? http://bit.ly/2gfy5hO

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Power App is a Google Chrome extension that has a description of "This extension configures your Default Search to Power App (searchpowerapp.com)".

This article was published first at Remove the Power App Chrome Extension